Re: [Wien] Problem with wien2k 13.1 parallel for Slurm+intel mpi
Dear Prof. Blaha, thanks a lot for your reply. I have corrected the .machines file (the node with 6 cores is automatically chosen): - lapw0: alcc92:6 1:alcc92:6 granularity:1 extrafine:1 - but nevertheless got the following output in case.dayfile: ---case.dayfile Calculating case in /alcc/gpfs1/home/exp6/pavlenna/work/laosto/ovac/case on alcc92 with PID 9804 using WIEN2k_13.1 (Release 17/6/2013) in /alcc/gpfs1/home/exp6/pavlenna/wien start (Tue Nov 26 13:41:14 CET 2013) with lapw0 (50/99 to go) cycle 1 (Tue Nov 26 13:41:14 CET 2013) (50/99 to go) lapw0 -p(13:41:15) starting parallel lapw0 at Tue Nov 26 13:41:15 CET 2013 .machine0 : 6 processors 0.024u 0.024s 0:12.00 0.3% 0+0k 1632+8io 6pf+0w lapw1 -up -p (13:41:27) starting parallel lapw1 at Tue Nov 26 13:41:27 CET 2013 - starting parallel LAPW1 jobs at Tue Nov 26 13:41:27 CET 2013 running LAPW1 in parallel mode (using .machines) 1 number_of_parallel_jobs alcc92 alcc92 alcc92 alcc92 alcc92 alcc92(6) 0.016u 0.004s 0:00.75 1.3%0+0k 0+8io 0pf+0w Summary of lapw1para: alcc92k=0 user=0 wallclock=0 0.068u 0.020s 0:02.19 3.6% 0+0k 0+104io 0pf+0w lapw1 -dn -p (13:41:29) starting parallel lapw1 at Tue Nov 26 13:41:29 CET 2013 - starting parallel LAPW1 jobs at Tue Nov 26 13:41:29 CET 2013 running LAPW1 in parallel mode (using .machines.help) 1 number_of_parallel_jobs alcc92 alcc92 alcc92 alcc92 alcc92 alcc92(6) 0.020u 0.004s 0:00.42 4.7%0+0k 0+8io 0pf+0w Summary of lapw1para: alcc92k=0 user=0 wallclock=0 0.072u 0.028s 0:02.11 4.2% 0+0k 0+104io 0pf+0w lapw2 -up -p(13:41:31) running LAPW2 in parallel mode ** LAPW2 crashed! 0.248u 0.012s 0:00.73 34.2% 0+0k 8+16io 0pf+0w error: command /alcc/gpfs1/home/exp6/pavlenna/wien/lapw2para -up uplapw2.def failed stop error - In the uplapw2.err I have the following error messages: Error in LAPW2 'LAPW2' - can't open unit: 30 'LAPW2' -filename: case.energyup_1 ** testerror: Error in Parallel LAPW2 - and the following error output messages: -- starting on alcc92 LAPW0 END LAPW0 END LAPW0 END LAPW0 END LAPW0 END LAPW0 END Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator case.scf1up_1: No such file or directory. grep: No match. Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator case.scf1dn_1: No such file or directory. grep: No match. FERMI - Error cp: cannot stat `.in.tmp': No such file or directory stop error --- Please let me know, maybe something is wrong in the mpi configuration. I have an intel mpi installed on the cluster. Best regards, N.Pavlenko Am 2013-11-23 13:07, schrieb Peter Blaha: You completely misunderstand how parallelization in wien2k works. Please read the UG carefully (parallelization), also notice the
Re: [Wien] Problem with wien2k 13.1 parallel for Slurm+intel mpi
The PMPI_Comm_size: Invalid communicator, error stack is almost always due to issues with how the mpi version was compiled and linked. Common issues include: 1) Not using the ifort/icc mpi compilers. 2) Not using the correct linking options for the flavor of mpi that you are using 3) Problems with the infiniband or similar drivers on the system (rare, but not unknown). For 1), please check that the mpif77 (or mpif90) you used is the Intel one -- you may need to source the scripts in the Intel bin directory to set these up correctly. For 2), the Intel Math Kernel Library at http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor is useful. N.B., I susect that lapw0_mpi did not run, as well as lapw1_mpi. On Tue, Nov 26, 2013 at 7:03 AM, Natalia Pavlenko natalia.pavle...@physik.uni-augsburg.de wrote: Dear Prof. Blaha, thanks a lot for your reply. I have corrected the .machines file (the node with 6 cores is automatically chosen): - lapw0: alcc92:6 1:alcc92:6 granularity:1 extrafine:1 - but nevertheless got the following output in case.dayfile: ---case.dayfile Calculating case in /alcc/gpfs1/home/exp6/pavlenna/work/laosto/ovac/case on alcc92 with PID 9804 using WIEN2k_13.1 (Release 17/6/2013) in /alcc/gpfs1/home/exp6/pavlenna/wien start (Tue Nov 26 13:41:14 CET 2013) with lapw0 (50/99 to go) cycle 1 (Tue Nov 26 13:41:14 CET 2013) (50/99 to go) lapw0 -p(13:41:15) starting parallel lapw0 at Tue Nov 26 13:41:15 CET 2013 .machine0 : 6 processors 0.024u 0.024s 0:12.00 0.3% 0+0k 1632+8io 6pf+0w lapw1 -up -p (13:41:27) starting parallel lapw1 at Tue Nov 26 13:41:27 CET 2013 - starting parallel LAPW1 jobs at Tue Nov 26 13:41:27 CET 2013 running LAPW1 in parallel mode (using .machines) 1 number_of_parallel_jobs alcc92 alcc92 alcc92 alcc92 alcc92 alcc92(6) 0.016u 0.004s 0:00.75 1.3%0+0k 0+8io 0pf+0w Summary of lapw1para: alcc92k=0 user=0 wallclock=0 0.068u 0.020s 0:02.19 3.6% 0+0k 0+104io 0pf+0w lapw1 -dn -p (13:41:29) starting parallel lapw1 at Tue Nov 26 13:41:29 CET 2013 - starting parallel LAPW1 jobs at Tue Nov 26 13:41:29 CET 2013 running LAPW1 in parallel mode (using .machines.help) 1 number_of_parallel_jobs alcc92 alcc92 alcc92 alcc92 alcc92 alcc92(6) 0.020u 0.004s 0:00.42 4.7%0+0k 0+8io 0pf+0w Summary of lapw1para: alcc92k=0 user=0 wallclock=0 0.072u 0.028s 0:02.11 4.2% 0+0k 0+104io 0pf+0w lapw2 -up -p(13:41:31) running LAPW2 in parallel mode ** LAPW2 crashed! 0.248u 0.012s 0:00.73 34.2% 0+0k 8+16io 0pf+0w error: command /alcc/gpfs1/home/exp6/pavlenna/wien/lapw2para -up uplapw2.def failed stop error - In the uplapw2.err I have the following error messages: Error in LAPW2 'LAPW2' - can't open unit: 30 'LAPW2' -filename: case.energyup_1 ** testerror: Error in Parallel LAPW2 - and the following error output messages: -- starting on alcc92 LAPW0 END LAPW0 END LAPW0 END LAPW0 END LAPW0 END LAPW0 END Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator case.scf1up_1: No such file or directory. grep: No match. Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123): MPI_Comm_size(comm=0x5b, size=0x7e356c) failed PMPI_Comm_size(76).: Invalid communicator Fatal error in PMPI_Comm_size: Invalid communicator, error stack: PMPI_Comm_size(123):
[Wien] Exchange-correlation energy
Dear Wien2k users, Some time ago there was discussed topic about xc energy http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01719.html. Since then Wien2k has KVC flag allowing to print :EXC contribution to the total energy. Could you please navigate me how: 1. one gets separate exchange and correlation contributions? 2. to get the separate contributions orbital resolved for each atom in the cell? 3. to get the xc contributions in a particular region (say cylinder = including part of interstitial and muffin-tins) of the cell? I would like to do it for PBE (option 13). Thanks in advance for help. Martin Gmitra Uni Regensburg ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Exchange-correlation energy
Hi, For 1 there is IGRAD.EQ.33 in vxclm2.f which is for exchange-only PBE (then correlation c is c=xc-x). For such thing the correct procedure is to plug the PBE orbitals (obtained from an usual PBE calculation) into the exchange-only PBE: 1) replace 13 by 33 in case.in0 2) x lapw0 I' m not really sure to understand for 2. For 3 there is the contributions from the spheres and interstitial in case.output0. This is the 3rd column when you grep for TOTAL= (the values are in Hartree). This is not really possible to get easily the contrbution from an arbitrary region of space. A solution would be to use lapw5 to write on a file the values of exc on a regaular 3d grid an then integrate yourself. But then the integration close to the nuclei will be very inaccurate. One thing: It is dangerous and not recommended to compare two values of Exc when they were obtained from two different electron densities. F. Tran On Tue, 26 Nov 2013, Martin Gmitra wrote: Dear Wien2k users, Some time ago there was discussed topic about xc energy http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01719.html. Since then Wien2k has KVC flag allowing to print :EXC contribution to the total energy. Could you please navigate me how: 1. one gets separate exchange and correlation contributions? 2. to get the separate contributions orbital resolved for each atom in the cell? 3. to get the xc contributions in a particular region (say cylinder = including part of interstitial and muffin-tins) of the cell? I would like to do it for PBE (option 13). Thanks in advance for help. Martin Gmitra Uni Regensburg ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Slab dielectric function vs. bulk dielectric function
Dear Prof. Blaha, Thank you for your suggestion. I tried using hexagonal structure of bulk Al with 39 MLs and 61x61x1 k-mesh. Actually I can reproduce plasma frequency and dielectric function compared to the results from one Al atom unit cell calculations. I plotted the calculated slab plasma frequency as a function of Al(111) film thickness and find the value is approaching converged, even though the converged value is 2eV smaller the plasma frequency from bulk geometry calculation. For the thickness dependence of dielectric function, I also get the similar converged results. The sizable difference lies at the low energy range(1.2eV). it converges to bulk value at large energy range, say, of 2.5eV. I am trying to do a very dense k-mesh calculation, (e.g. 99x99x1). However this dense mesh does not sound practical. Thank you again, Wenmei 2013/11/25 Peter Blaha pbl...@theochem.tuwien.ac.at Of course, in principle slabs should converge to bulk epsilon. But: In your slabs with a k-mesh of 69x69x1 you are using effectively a k-mesh of 69x69x39 instead of a 69x69x69 mesh. In addition, in the z direction you use root-sampling instead of tetrahedra method. It is like integration with the rectangular-rule instead of a trapezoidal rule. Try fcc-Al with a small tetragonal distortion during setup, so that you get only 16 sym.ops. then change c/a back to 1 and use a kmesh of 69x69x39 and compare the dielectric function to the 2 times 69-mesh. (This mimics the k-mesh problem, but still there s the integration method !!). You probably need even more layers Am 26.11.2013 04:51, schrieb phlhj phlhj: Dear Prof. Blaha, Thanks so much for your suggestion. I tried bulk Al supercell with 39ML without vacuum with the same k-mesh as used in 39 ML thin film supercell. In fact I get the same results for plasma frequency and dielectric function as those from Al unit cell with only one Al atom. I think the k-mesh of 61x61x1 I used in my calculation is dense enough to give a precise result. The main difference for the dielectric function between thin film geometry and bulk geometry is at the low energy range (1.2eV). I researched some paper for studying the anisotropic surface reflectance in semiconductor surface, say, GaAs(110). Even 15 atomic layers are used in the LDA calculation but still some difference around the band gap regime for the dielectric function is found between surface calculation and bulk calculation. I think the difference I encountered for teh dielectric function between slab Al(111) and bulk Al might be similar to the case in semiconductor system. However, from the physical point of view, it's hard to understand why there is still appreciable difference out there even though very thick film is used. Physically the dielectric function of the very thick slab should converge to that in the bulk counterpart. Thank you so much for sharing any understanding about this, Wenmei 2013/11/24 Peter Blaha pbl...@theochem.tuwien.ac.at mailto: pbl...@theochem.tuwien.ac.at As you probably know, the dielectric function of Al converges VERY slowly with respect to the k-mesh. When you do slab calculations, you include the surface effect, but you also replace the periodicity in k-z (and thus the k-mesh in k-z) to a backfoldung according to your slab. Even a 39 ML slab corresponds probably not to a very large k-z mesh and in addition the integration over k-z is limited to a root-sampling instead of the tetrahedron method. I could even imagine large numerical problems in this 2-D integration using a 3-D algorithm in joint due to large degeneracy of the tetrahedra. At least you could differentiate between integration problems and surface effects by using a 39-layer bulk structure (i.e. remove the vacuum in your supercell, so that you get 3D-Al again, but restrict yourself to 1-k point in k-z) and compare the resulting eps to bulk Al (with 1 atom/cell and good k-meshes. Am 23.11.2013 16:54, schrieb phlhj phlhj: Dear all, I was trying to calculate the optical properties of Al(111) slab. For the bulk FCC Al, I can reproduce the dielectric functions and plasma frequency very precisely reported in literature before. However, I did find some difference between the slab dielectric functions and the corresponding bulk values. Especially even though I used very thick slab, say 39MLs, in the low photo energy range (1eV), the imaginary part is much larger than the bulk. I doubt this may be related to the band-folding and symmetry reduction in the direction normal to the surface. Also, I found the plasma frequency of the slab is smaller than the bulk plasma frequency. Mathematically, this behavior of the imaginary parts of the interband and intraband transitions contributions seems to be able to be
[Wien] LSDA+U+SO orbital moment and spin moment
Hello, everyone. I use wien2k with LSDA+U+SO method to calculate the AFM. And set the direction of magnetization in (1,0,0). However, I found that spin moment and orbital moment not only had x component but also had y component. At sometime, the y component was larger than x direction. My question is how do I select the spin moment and orbital momet? Should I just take the PROJECTION one or take three direction into consideration? And how do I determine the magnetic moment direction? Is the direction in the file *.inso or determined by output in *.scf(i.e. SPIN MOMENT: -0.25635 0.00270 0.0 )? thank you very much! *** :SPI019: SPIN MOMENT: -0.25635 0.00270 0.0 PROJECTION ON M -0.25635 :SPI020: SPIN MOMENT: 0.25636 -0.00270 0.0 PROJECTION ON M 0.25636 :SPI021: SPIN MOMENT: 0.25675 0.00286 0.0 PROJECTION ON M 0.25675 :SPI022: SPIN MOMENT: -0.25675 -0.00286 0.0 PROJECTION ON M -0.25675 :SPI023: SPIN MOMENT: 2.66505 0.00241 0.0 PROJECTION ON M 2.66505 :SPI024: SPIN MOMENT: -2.66505 -0.00241 0.0 PROJECTION ON M -2.66505 :SPI025: SPIN MOMENT: -2.66425 0.00239 0.0 PROJECTION ON M -2.66425 :SPI026: SPIN MOMENT: 2.66425 -0.00239 0.0 PROJECTION ON M 2.66425 :ORB019: ORBITAL MOMENT: -0.03831 -0.01570 0.0 PROJECTION ON M -0.03831 :ORB020: ORBITAL MOMENT: 0.03831 0.01570 0.0 PROJECTION ON M 0.03831 :ORB021: ORBITAL MOMENT: 0.03811 -0.01582 0.0 PROJECTION ON M 0.03811 :ORB022: ORBITAL MOMENT: -0.03811 0.01582 0.0 PROJECTION ON M -0.03811 :ORB023: ORBITAL MOMENT: -0.35968 0.71525 0.0 PROJECTION ON M -0.35968 :ORB024: ORBITAL MOMENT: 0.35968 -0.71525 0.0 PROJECTION ON M 0.35968 :ORB025: ORBITAL MOMENT: 0.35830 0.71689 0.0 PROJECTION ON M 0.35830 :ORB026: ORBITAL MOMENT: -0.35830 -0.71689 0.0 PROJECTION ON M -0.35830 *___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
